This Certificate is being
delivered pursuant to the requirements of Section 1350 of Chapter 63 (Mail Fraud) of Title 18 (Crimes and Criminal Procedures) of the United States Code and shall not be relied on by any person for any other purpose.

The undersigned, who are the Chief Executive Officer and Chief Financial Officer, respectively, of Manhattan Associates, Inc. (the
Company), hereby each certify that, to the undersigneds knowledge:

The Quarterly Report on Form 10-Q of the
Company for the quarterly period ended June 30, 2012 (the Report), which accompanies this Certification, fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934, and all information
contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Dated this
6th day of August, 2012

/s/ Peter F. Sinisgalli

Peter F. Sinisgalli, Chief Executive Officer and Director

/s/ Dennis B. Story

Dennis B. Story, Executive Vice President, Chief Financial

Officer and Treasurer

In accordance with SEC Release No. 34-47986, this Exhibit is furnished to the SEC as an accompanying document
and is not deemed filed for purposes of Section 18 of the Securities Exchange Act of 1934 or otherwise subject to the liabilities of that Section, nor shall it be deemed incorporated by reference into any filing under the Securities
Act of 1933. A signed original of this written statement required by Section 906 of the Sarbanes-Oxley Act of 2002 has been provided to the registrant and will be retained by the registrant and furnished to the Securities and Exchange
Commission or its staff upon request.